Create Series Info File for GXPA
Usage
make_series_info_file(
filename,
series_name,
series_descript,
default_group,
organism,
expr_units,
pmid = NULL,
analyst = NULL,
analyst_comments = NULL,
default_color = NULL,
extra.list = NULL
)
Arguments
- filename
series info output file name
- series_name
series name (can match series name used in GXPA app)
- series_descript
series description
- default_group
default group to consider for plots (will often be used for x axis variable)
- organism
series organism
- expr_units
data experimental units
- pmid
PubMed id (can be NULL)
- analyst
data analyst (can be NULL)
- analyst_comments
comments by analyst (can be NULL)
- default_color
default color to consider for plots (can be NULL)
- extra.list
named list of extra variables to include in the series info file
Examples
filename <- tempfile(fileext = ".csv")
make_series_info_file(
file = filename,
series_name = "SU2C_2019",
series_descript = "Long description",
default_group = "tumor_site",
organism = "human",
expr_units = "RNA seq log2 (FPKM+1)",
pmid = 31061129,
default_color = "AR_score_group",
extra.list = list(
"Extra_Field" = "Something",
"Another_one" = 5
)
)
utils::read.csv(filename)
#> key value
#> 1 series_name SU2C_2019
#> 2 series_descript Long description
#> 3 default_group tumor_site
#> 4 organism human
#> 5 expr_units RNA seq log2 (FPKM+1)
#> 6 pmid 31061129
#> 7 default_color AR_score_group
#> 8 Extra_Field Something
#> 9 Another_one 5